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Citation: Lijia Jia,  Jianjun Chen,  Haizhou Liu,  Wenhui Fan,  Depeng Wang,  Jing Li,  Di Liu. Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain [J].VIROLOGICA SINICA.  http://dx.doi.org/10.1007/s12250-020-00217-2

Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain

  • Corresponding author: Jing Li, lj418@163.com
  • Received Date: 05 January 2020
    Accepted Date: 07 March 2020
    Published Date: 08 April 2020

    Fund Project: This work was supported by the Research Project of African Swine Fever of Chinese Academy of Sciences (KJZD-SWL06), the National Natural Science Foundation of China (31941015), the National Key R&D Program of China (2016YFC1200800 & 2018YFC0840402), the China Mega-Project for Infectious Disease (2017ZX10103005-005), the State Key Laboratory of Veterinary Biotechnology Research Fund (SKLVBF201902). J.L. is supported by Youth Innovation Promotion Association of CAS (2019091). We acknowledge Lei Zhang (the Center for Instrumental Analysis and Metrology in the Wuhan Institute of Virology, CAS) for supporting in the genome sequencing.

  • It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August 2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019). ASF is an acute febrile, hemorrhagic and fulminating infectious disease, and would reach 100% case fatality rate to pigs (Gallardo et al. 2015). The causative pathogen, African swine fever virus (ASFV), is a doublestranded DNA virus with a genome of 170–193 kb belonging to the Asfarviridae family (Galindo and Alonso 2017; Gallardo et al. 2015). A recent study has revealed that ASFV maintains a core genome of 102 ORFs and has 168 dispensable genes (Wang et al. 2019). Thus, the complexed genomic features of ASFV require more attentions. By using the next generation sequencing (NGS) and the single molecule real-time sequencing (SMRT-seq), a couple of Chinese ASFV genomes have been uncovered (Bao et al. 2019; Wen et al. 2019; Jia et al. 2019). Compared to NGS, SMRT-seq has the advantage of long read length and can generate sequencing data containing the original single base modification information, which can be identified through the state-of-art bioinformatic procedures (Senol Cali et al. 2019; Simpson et al. 2017). DNA methylation is a chemical modification common in animal and plant genomes. It refers to the catalytic transfer of methyl groups on active methyl compounds (such as s-adenosine methionine) to other compounds under the catalysis of DNA methyltransferase (DNMT), mainly forming 5-methylcytosine (5-mC), 6-methyladenine (6-mA), 5-hydroxymethylcytosine (5-hmC), etc. DNA methylation, which triggers the epigenetic regulatory mechanism, has been proved to play important roles in gene expression and regulation, embryonic development, and disease-related aspects (Gouil and Keniry 2019). Whether ASFV genome has DNA methylation and epigenetic regulation is to be discerned.

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    Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain

      Corresponding author: Jing Li, lj418@163.com
    • 1 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
    • 2 Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
    • 3 African Swine Fever Regional Laboratory of China, Wuhan 430071, China
    • 4 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
    • 5 NextOmics Biosciences, Wuhan 430074, China
    • 6 Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China
    • 7 University of Chinese Academy of Sciences, Beijing 100049, China
    Fund Project:  This work was supported by the Research Project of African Swine Fever of Chinese Academy of Sciences (KJZD-SWL06), the National Natural Science Foundation of China (31941015), the National Key R&D Program of China (2016YFC1200800 & 2018YFC0840402), the China Mega-Project for Infectious Disease (2017ZX10103005-005), the State Key Laboratory of Veterinary Biotechnology Research Fund (SKLVBF201902). J.L. is supported by Youth Innovation Promotion Association of CAS (2019091). We acknowledge Lei Zhang (the Center for Instrumental Analysis and Metrology in the Wuhan Institute of Virology, CAS) for supporting in the genome sequencing.

    Abstract: It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August 2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019). ASF is an acute febrile, hemorrhagic and fulminating infectious disease, and would reach 100% case fatality rate to pigs (Gallardo et al. 2015). The causative pathogen, African swine fever virus (ASFV), is a doublestranded DNA virus with a genome of 170–193 kb belonging to the Asfarviridae family (Galindo and Alonso 2017; Gallardo et al. 2015). A recent study has revealed that ASFV maintains a core genome of 102 ORFs and has 168 dispensable genes (Wang et al. 2019). Thus, the complexed genomic features of ASFV require more attentions. By using the next generation sequencing (NGS) and the single molecule real-time sequencing (SMRT-seq), a couple of Chinese ASFV genomes have been uncovered (Bao et al. 2019; Wen et al. 2019; Jia et al. 2019). Compared to NGS, SMRT-seq has the advantage of long read length and can generate sequencing data containing the original single base modification information, which can be identified through the state-of-art bioinformatic procedures (Senol Cali et al. 2019; Simpson et al. 2017). DNA methylation is a chemical modification common in animal and plant genomes. It refers to the catalytic transfer of methyl groups on active methyl compounds (such as s-adenosine methionine) to other compounds under the catalysis of DNA methyltransferase (DNMT), mainly forming 5-methylcytosine (5-mC), 6-methyladenine (6-mA), 5-hydroxymethylcytosine (5-hmC), etc. DNA methylation, which triggers the epigenetic regulatory mechanism, has been proved to play important roles in gene expression and regulation, embryonic development, and disease-related aspects (Gouil and Keniry 2019). Whether ASFV genome has DNA methylation and epigenetic regulation is to be discerned.

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